I first paint the ship to look like it has been freshly painted. Then I take separate batches of color that have been lightened or darkened and slightly mottle the color- lighter for highlights and darker for shadow areas and depressions- just to add depth. Then I add darker washes to further accent details, followed by dry brushing with a lighter color for highlights. I've noticed that hulls and splinter shields of ships that have been at sea for extended periods are lighter on the bottoms. I've finally concluded that this is from buildup of salt deposits- spray hits the plates and the water evaporates as it drips down leaving salts and mineral deposits on the lower portions. The same goes for hulls where the swell runs along the waterline.

Obviously less pronounced the higher you get. Decks have traffic areas where the paint is kept closer to fresh by the wear from the crew's shoes. Non-traffic areas have more oxidation and are lighter. Runoff from the upper decks will stain the lower decks, too. After I get the paint faded the way I want it then I'll go ahead and give it a coat of flat clear to seal that step in preparation for the next step...rust. I like to use water colors. I have a 10-color kid's set that I use all the time. Just mix black, browns, white, yellow and orange in varying amounts using the inside of the paint set lid for a palette. Use less water so it doesn't just bead up when you apply the paint.

You have to remember that it isn't all rust either. There is also oil from machinery, paint oxidation that washes off and plain old grime. Look at old cars and trucks for inspiration if you can't get to a marina or harbor to see real ships or work boats. Rust is rust. 

You can apply the water colors heavily as long as the tints and tones are about what you're looking for. Put them on with a larger brush or cotton swab. Apply it a little heavier where water is most likely to drain or where things might rub together- hawse pipes, for instance. After these are dry, I'll go back with moistened swabs (water or Windex) and erase most of the watercolor.

This is where you pull it back to make it subtle. You can leave it heavier in some places to represent areas where heavy rust builds up; very faint like it's just a stain; or erase it completely where you've changed your mind. The clear coat protects the base paint. Then I'll do a little more dry brushing with the original or lighter base color to put back in the highlights.

Finally, I lightly airbrush around the rust areas with the original and lighter base colors to further take the edge off the rust. The way I look at it, rust doesn't occur all at once and it has different effects in different areas. There is also a difference between areas where rust and grime have been deposited and where paint has gotten water under it and rusted through. Going back and forth with the base colors and rust gives the impression that the rust has built up over time.

I would also advise against heavily weathering and rusting the upper works. Deck crews are usually tasked to chasing those areas down and keeping them as shipshape as possible depending on service conditions- even under way. There are exceptions, of course, especially in northern areas of the Atlantic and Pacific oceans. Faded paint is common but rust is usually dealt with promptly. They can't get at the hull until they anchor somewhere and can put a chair over the side.

If you are doing a full-hull ship, don't forget the barnacles and paint fading there, too. I had a hard drive crash and lost the URL and pics of the  Spruance class DD that got rammed, but there were excellent references for hull weathering on that site. Mix up some paint that is dark green (almost black), lower your air pressure, open the nozzle and splatter the barnacles on. I apply them a little heavier along the waterline and in depressions to add depth. Remember to mask the hull above where the water normally reaches.

By the , using watercolors like this also works for oil stains and fuel spills around filler caps on aircraft. Of course, these tips work better on larger scales. The important thing is to keep weathering subtle or it will overwhelm all of your other modeling efforts. Exercise restraint. Too little weathering is better than too much.